BioC 3.6: CHECK report for GenomicRanges on veracruz1

Package: GenomicRanges

Version: 1.29.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicRanges_1.29.12.tar.gz

StartedAt: 2017-08-16 03:36:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:41:34 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 280.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicRanges.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicRanges_1.29.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.29.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicRanges’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{reduce}{GenomicRangesList}
  Code: function(x, drop.empty.ranges = FALSE, ...)
  Docs: function(x, drop.empty.ranges = FALSE, min.gapwidth = 1L,
                 with.inframe.attrib = FALSE, ignore.strand = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    min.gapwidth with.inframe.attrib ignore.strand
  Mismatches in argument names:
    Position: 3 Code: ... Docs: min.gapwidth

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
genomicvars              55.875 14.758  73.123
GPos-class               29.963  3.264  34.164
makeGRangesFromDataFrame  1.707  0.049  19.645
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicRanges’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c transcript_utils.c -o transcript_utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)

name	user	system	elapsed
GNCList-class	1.143	0.014	1.209
GPos-class	29.963	3.264	34.164
GRanges-class	1.656	0.012	1.711
GRangesList-class	0.569	0.005	0.590
GenomicRanges-comparison	0.306	0.004	0.314
absoluteRanges	1.632	0.130	1.866
constraint	1.193	0.021	1.258
coverage-methods	0.237	0.001	0.244
findOverlaps-methods	1.196	0.015	1.235
genomic-range-squeezers	0.000	0.000	0.001
genomicvars	55.875	14.758	73.123
inter-range-methods	2.571	0.360	3.076
intra-range-methods	0.549	0.004	0.622
makeGRangesFromDataFrame	1.707	0.049	19.645
makeGRangesListFromDataFrame	0.131	0.006	0.149
nearest-methods	0.835	0.010	0.873
phicoef	0.036	0.000	0.037
setops-methods	2.751	0.013	2.894
strand-utils	0.117	0.004	0.124
tile-methods	0.113	0.002	0.118
tileGenome	0.293	0.010	0.307